Antibodies are molecules that circulate around the body as part of the immune system. These molecules are individually designed to bind to specific foreign substances, which are known as antigens. Individual antigens have specific shapes and chemical make-up, so antibodies have specifically shaped binding sites to fit the antigen. The strength of the bond between an antigen and a binding site on an antibody is called antibody affinity. Generally, the stronger this affinity is, the more effective the antibody can be at recognizing the invader.

Every biological organism or portion of an organism is made up of organic molecules. The arrangement and amount of these molecules is specific to the organism. For example, a bacterial cell has a structural cell membrane that has a variety of molecules stuck into it, which each do a specific job. Some may bind to environmental substances to bring them into the cell, whereas other external molecules may help to attach the bacterium to a host cell during an invasion of a host.

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The human body has evolved a system of cells and molecules that police the body and check for invaders. Antibodies are not cells, but rather molecules that float around, waiting to come across invaders or bits of invaders. The antibody population is made up a a wide variety of molecules, each specially structured to fit onto a particular type of molecule, such as the external molecules on the outside of a bacterial cell. After the body is exposed to a pathogen, such as the measles virus, and manages to clear the infection, it has a memory of the type of antigens present on the virus, producing specialized antibodies specifically to fight another infection by the pathogen.

These specialized antibodies have a specific shape to their binding sites, which fit the virus particle antigens perfectly. The strength of bonding between one binding site on an antibody to one antigen on the invader is known as the antibody affinity of that binding site. When looking at more than one binding site on the antibody, the strength of the bond between the sites and the invader is known as the avidity, or the functional affinity of the antibody.

At their simplest, antibodies and antigens are collections of atoms, which are held together with chemical bonds. The type of bonds that hold an antigen to an antibody are non-covalent bonds, which means that the individual atoms and molecules do not share any of their electron particles, but rather hold together through forces like weak electric attraction. Normally, bonds that do not involve the movement of electrons from one molecule to another are relatively weak, but a collection of lots of non-covalent bonds can be strong. This situation occurs in antibody-antigen interactions, and is the basis for antibody affinity.

Antibody affinity strength is important for the efficient identification of invaders and the subsequent clearance of infection. Vaccines tend to produce strong antibody affinity to their antigens, as the antigens are derived specifically from the target pathogen, and engineered to be very recognizable. Despite the advantages to strong antibody affinity, however, the body is able to benefit from weak antibody affinities, as these can let the body recognize new invaders that are similar in some way to previously recognized invaders.

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